The Illumina NovaSeq 6000 Integration Package v3.7.0 supports the integration of Clarity LIMS to NovaSeq 6000 instruments. This documentation describes the integration and includes the following information:
Preconfigured workflows, protocols, steps, and automations
Installed components
Configuration requirements, rules, and constraints
For instructions on user interaction for each step, validating and troubleshooting the NovaSeq 6000 Integration, refer to .
The configuration provided in this integration has been established to support NovaSeq 6000 lab processes. Any configuration changes to protocols or workflows - including renaming protocols, steps, and fields - could break process.
Importing either the Library Prep Validation v2.3.4 workflow or the NovaSeq 6000 v3.8 workflows provides a global field named Illumina Universal Sample Identifier. This is a text field that is reserved for CLPA support and is optional. A value is not required for this integration.
Prerequisites and Assumptions
It is assumed that samples enter the NovaSeq 6000 v3.8 workflow as normalized libraries. It is assumed that the following steps have completed before samples are assigned to the workflow:
Samples have been accessioned into the Clarity LIMS.
Samples have been run through QC and library prep.
Samples have been normalized, and the value is captured in a field called Normalized Molarity (nM).
For more information on sample accessioning, refer to Sample Accessioning and Upload and Modify Samples in the Getting Started section of the .
You can assign samples to workflows automatically, using a routing script, or manually—from the Projects & Samples dashboard. Refer to Assign and Process Samples in the .
Workflows, Protocols, and Steps
The Illumina NovaSeq 6000 Integration Package v3.7.0 includes the following workflows:
Library Prep Validation v2.3.4 (optional, but recommended for validation purposes)
NovaSeq 6000 v3.8
Library Prep Validation v2.3.4 Workflow
Protocol: Library Prep Validation v2.3.4
Purpose:
Included for validation purposes only, this protocol models the library prep steps required to advance samples to the Run Format (NovaSeq 6000 v3.8) protocol.
The protocol contains a single step - Library Prep Validation v2.3.4. After this step, a routing script sends the samples to the first step of the NovaSeq 6000 v3.8 workflow - Define Run Format (NovaSeq 6000 v3.8).
Steps:
Library Prep Validation v2.3.4
NovaSeq 6000 v3.8 Workflow
Protocol 1: Run Format (NovaSeq 6000 v3.8)
Purpose:
Allows for the assignment of per sample values for:
Loading Workflow Type: Select either NovaSeq Standard or NovaSeq Xp.
Normalized Molarity: Enter a value for each sample.
Flowcell Type: Select from options SP, S1, S2, or S4.
Final Loading Concentration (pM): Select from options 225 (PCR-free workflows) or 400 (Nano workflows), or enter a different value.
Compares the Normalized Molarity value of each sample with the Minimum Molarity value.
Routing script sends samples to the NovaSeq Standard or NovaSeq Xp protocol, according to the selected Loading Workflow Type.
Samples with Normalized Molarity less than Minimum Molarity are removed from the workflow.
Steps:
Define Run Format (NovaSeq 6000 v3.8)
Protocol 2: NovaSeq Standard (NovaSeq 6000 v3.8)
Purpose:
Samples are pooled and added to the library tube in preparation for the NovaSeq run. The run setup information is validated and a sample sheet is generated.
Routing script sends the library tube to the AUTOMATED - NovaSeq Run (NovaSeq 6000 v3.8) protocol.
Steps:
Make Bulk Pool for NovaSeq Standard (NovaSeq 6000 v3.8)
Dilute and Denature (NovaSeq 6000 v3.8)
Protocol 3: NovaSeq Xp (NovaSeq 6000 v3.8)
Purpose:
Samples are pooled and added to lanes on the NovaSeq flow cell. The option selected in the Define Run Format (NovaSeq 6000 v3.8) step determines the flow cell type. The run setup information is validated and a sample sheet is generated.
Routing script sends flow cell to the AUTOMATED - NovaSeq Run (NovaSeq 6000 v3.8) protocol.
Steps:
Make Bulk Pool for NovaSeq Xp (NovaSeq 6000 v3.8)
Dilute, Denature & ExAmp (NovaSeq 6000 v3.8)
Load to Flowcell (NovaSeq 6000 v3.8)
Protocol 4: AUTOMATED - NovaSeq Run (NovaSeq 6000 v3.8)
Purpose:
All samples complete the workflow by going through this protocol.
This protocol contains one fully automated step.
⚠ Do not add samples to the Ice Bucket or start the step. The integration starts the step automatically.
